Hello Max,
Thank you for bringing this to our attention. I have added the file and
updated the wiki.
Cheers,
--Luis
On Sat, Feb 17, 2024 at 9:20 AM Max Brazhnikov
wrote:
> Hi all,
>
> pepXML_v123.xsd was committed almost two years ago [1], however pepXML
> wiki page [2] has ceased at v1.22,
Hi Sam,
It does sound like potentially an issue with the mzML file path(s) inside
the comet pepXML results, though there could be other issues.
As for troubleshooting, you can inspect the URL of those troublesome links
and look for the Dta= (or File=) parameter -- is the filepath the same that
Hello Alex,
Glad that you were able to get to the bottom of this issue and hope you
have been able to process your data.
I just wanted to add that when installing TPP on Windows, the entire
ProteoWizard set of tools (including msConvert GUI) is also bundled -- so
there is typically no need to
Hi Will,
Thanks for the reply and extra info. This strange redirects may be
connected to IT changes that took place recently; I'll follow up with them.
--Luis
On Fri, Jan 12, 2024 at 9:57 AM Will Comstock wrote:
> Thanks Luis, your direct link works for me!
>
> Looks like clicking the
Hello Tanmay,
How did you generate the input pepXML files? Which search engine did you
use? Are you able to open both of those files and verify that they have
results?
Can you process results from another search engine (e.g. Comet or X!Tandem)
of the same mzML data?
Cheers,
--Luis
On Wed, Jul
Hi Emma,
The ProtXMLViewer is under the cgi-bin/ directory of the image. However,
the version in 6.2.0 does not have the command-line capability of exporting
protXML to TSV. We introduced this feature in 6.3.0, and will be available
once we produce the related image. (well, after fixing some
This should already be possible with, e.g.
variable_mod02 = 40.000 C 0 3 -1 0 0 0.0
add_C_cysteine = 50.000
(Of course using whatever masses are appropriate.)
Or does this not work?
On Mon, Jul 31, 2023 at 9:31 PM Debojyoti Pal
wrote:
> Thanks Luis. I have asked this on the COMET group as
Hi Debojyoti,
Yes, I would say this is the most straightforward way of conducting this
search.
Note that you may need to make further adjustments to the variable mod
string settings if, say, a given peptide must have *all* of its Cysteines
in one state (+50) or the other (+90). The default is to
Hello Carlo,
I recall seeing a report like this years ago, and I think it has to do with
configuring the Mascot server to open its port. I forget the details of
how this is done, and we don't have a Mascot server in-house where we can
test; perhaps someone else is able to provide help on this.
ear Luis,
>
> Please send the link of the registration form.
>
> Regards
>
> On Fri, Jul 21, 2023 at 1:42 PM 'Luis Mendoza' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
>> Hello Emma, Manuela, and others interested in attending virtually,
&g
Hello Emma, Manuela, and others interested in attending virtually,
We have decided to provide a remote option to attend the course via Zoom on
a limited basis. Please fill out and send me the registration form, and
note in the comments that you would like this option.
Please do note the
ity rules) on such
> short notice.
> Thanks,
> Don
>
> On Tue, Jul 18, 2023 at 3:44 PM 'Luis Mendoza' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
>> Hello all,
>> Based on the survey of dates that Eric sent out, we will hold a short TPP
>> c
Hello all,
Based on the survey of dates that Eric sent out, we will hold a short TPP
course next week, July 26 - 28, at ISB.
We will send a link to registration and more info in the next couple of
days, but expect to go 8am - 4:30pm on those three days.
Hope this date works for most of you!
--Luis
Hello Emma,
According to this, X!Tandem is indeed able to process MGF files:
https://www.thegpm.org/tandem/tandem_install_faq.html#faq6
Do note that the TPP GUI (Petunia) only allows you to choose mzML/mzXML
files as input, so you will have to run via the command-line. Also, any
downstream TPP
Hello everyone,
Next week the TPP software tools team will be attending and giving several
presentations at ASMS in Houston.
Please feel free to find us and say hello to me (Luis), David, and Michael,
and bring your PeptideAtlas/TPP-related software and/or installation
questions. We also have
Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.3.0
"Arcus"
We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP)
software, release 6.3.0. The software is available for Windows as well as
Linux from all the usual locations (please see the section below,
Hello Felipe,
There may be several reasons why you see the viral protein in your
analysis, e.g.
- Did you only run Comet, or did you validate using the TPP/Prophets?
If the latter, what was the probability of the protein(s) in question?
- What were the contents of the database that you
gt;
> Felipe
>
> El vie, 28 abr 2023 a las 4:58, 'Luis Mendoza' via spctools-discuss (<
> spctools-discuss@googlegroups.com>) escribió:
>
>> Hello Felipe,
>>
>> It is in general not normal to not find "any results" with TPP when other
>>
Hello Felipe,
It is in general not normal to not find "any results" with TPP when other
platforms do find some, as there is often partial, if not significant,
overlap. Typically when no results are found, it points to either bad data
(presumably not in this case) or incorrect parameters
Hi Will,
Glad you got this to work!
A potentially quicker solution is to enter those extra flags in the
"additional options" box in Petunia:
[image: image.png]
You can find a full set of available options at the Proteowizard msconvert
info page:
Sure thing.
And to answer your original question: there is a command-line tool in TPP
called batchcoverage (look in the bin/ directory) that calculates this
residue coverage -- and is the one used by ProteinProphet to populate that
attribute in protXML.
It needs an input file of the form:
Hello Yasir,
We have recently identified a bug in ProteinProphet that mis-reports the
coverage as zero for all proteins. This affects TPP versions 6.1.0 and
6.2.0. We will be releasing an update soon that corrects this and other
bugs.
Even then, the value that is reported in protXML is the
Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.2.0
"Nacreous"
We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP)
software, release 6.2.0. The software is available for Windows as well as
Linux from all the usual locations (please see the section
Hello,
The version of msconvert that is shipped with TPP is a couple of years old
and does not know about that instrument. You have three options to convert
your files:
1. Download and install a newer version of ProteoWizard, run the
conversion, and use that mzML file in Comet. This is likely
Hi,
Congrats on the new instrument, and happy holidays as well!
The error seems to indicate that there is no input data for ProteinProphet
to work with; can you verify that the input file contains validated search
results with probabilities above 0.2 ? Are there any other errors or
warnings in
Hello,
That is quite odd; Are you able to share a pepXML file so we can
troubleshoot? You can contact me directly to arrange a file transfer.
Thanks,
--Luis
On Tue, Oct 18, 2022 at 12:21 PM 2kl...@gmail.com <2kl...@gmail.com> wrote:
> Hi all,
>
> I am using the TPP v6.1.0 Parhelion, Build
Hi Will,
We tested it on Windows 11 a few months ago and noticed no issues. Please
do let us know if you run into any.
Cheers,
--Luis
On Thu, Oct 13, 2022 at 12:24 PM Will Comstock wrote:
> Hi all,
>
> Very quick question: Is the TPP 6.1.0 fully compatible with Windows 11?
>
> Thanks!
> -Will
rgetMS level = “3”). The quantification works now. Thanks
> for your help!!!
>
> Cheers,
> Yasir
>
> On Sep 8, 2022, at 6:15 PM, 'Luis Mendoza' via spctools-discuss <
> spctools-discuss@googlegroups.com> wrote:
>
> Hi Yasir,
> Is your data Thermo SPS where the report
Hello Yasir,
Can you try re-running Libra without the centroiding option? (i.e. set
type="0") Or are your mzML data not centroided?
Another thing to try: are you able to open the PeptideProphet + Libra
results in the PepXMLViewer? You should be able to see if there are a
significant number of
Hello Priti,
You can specify non-enzymatic cleavage by setting the *protein, cleavage
site* parameter to *[X]|[X]* .
More info at the X!Tandem site:
https://www.thegpm.org/TANDEM/api/pcs.html
https://www.thegpm.org/TANDEM/api/pcsemi.html
Hope this helps,
--Luis
On Wed, Aug 3, 2022 at 10:59 PM
Hello,
It seems that your issue may be caused by this parameter:
ms_level = 2-3 # MS level to analyze, valid are
levels 2 (default) or 3
Please specify it as a single value, e.g.
ms_level = *3* # MS level to analyze, valid are
levels 2 (default)
Hi Malcolm,
Yes, those instructions for adding new accounts are still valid; I find it
simplest to follow the ones under your second link ("TPP Login
Credentials").
Please do note that those passwords are only as secure as the server
protocol under which you install TPP -- i.e. things are not at
Very nice, thank you!
On Fri, Jun 10, 2022 at 4:18 PM Malcolm Cook wrote:
> I just finished successful install on CentOS7 with the following notes:
>
> https://github.com/malcook/tpp_sandbox/blob/main/tpp_install_centos7.org
>
> I hope it might help someone else
>
> On Monday, October 12,
Hi Malcolm,
Thank you for the congrats, and for catching that in our build notes; we
will correct it soon. In the "Pulling from Sourceforge" section, just
follow the commented-out command instead of the last one:
#svn checkout http://svn.code.sf.net/p/sashimi/code/tags/release_6.1.0
<-
Hello everyone,
The SPC software tools team will be leading an evening *Workshop on Monday
June 6th at 5:45pm in room M100 BC *during the ASMS Annual Conference.
We will give a brief intro to the existing TPP tools, including new
features in *TPP 6.1.0*, and then encourage discussion about them
Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.1.0
"Parhelion"
We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP)
software, release 6.1.0. The software is available for Windows as well as
Linux from all the usual locations (please see the section
Hello Max,
There seems to be an issue with running this command via the UI (Petunia).
Can you check if you get the same behavior when running on the command-line?
Thanks for reporting this.
--Luis
On Wed, Mar 2, 2022 at 3:56 PM Maxence Le Vasseur <
levasseurmaxe...@gmail.com> wrote:
> Hi there,
On Wed, Mar 2, 2022 at 3:56 PM Maxence Le Vasseur <
levasseurmaxe...@gmail.com> wrote:
> Hi there,
>
> It seems that the MzXML2Search function does not create .dta (and possibly
> other) files. Running the function from the Petunia web interface creates
> the folder but the folder is empty after
Hello Jill,
Yes, the TPP tools are run on your computer and no internet connection is
required other than to download it. Or you can install from a flash drive
or other similar media as well. The only time you might need internet is
to follow certain links to extra information from the various
Hello,
Is /usr/local/tpp/bin/ in your PATH? If not, please add it and try
again. You can test by typing which tpp_models.pl
We would also recommend installing the latest version of TPP (6.0.0), which
we recently released.
Hope this helps,
--Luis
On Mon, Aug 23, 2021 at 9:53 AM Huang
*Announcing the official release of Trans-Proteomic Pipeline (TPP) 6.0.0
"OmegaBlock".*
We are proud to offer a major update to the Trans-Proteomic Pipeline (TPP)
software, release 6.0.0. The software is available for Windows as well as
Linux from all the usual locations (please see the section
Hello Valdemir,
You can run the ProtXMLViewer on the command-line to do this.
If you want one protein per line, with peptides as a comma-separated list:
/FULL/PATH/TO/tpp/cgi-bin/ProtXMLViewer.pl -file
-action ExportExcel
If you want one peptide per line, with per-peptide stats as well:
Hello Laco,
The simplest way is to select the location of the data at the time you
install TPP. If you already installed TPP, you can just run the installer
again, making sure to specify the location of the data directory. (You can
leave the actual TPP installation in C:\TPP if you'd like).
Hello Giangiacomo,
You can use the Lib2html tool to convert an splib into a webpage with
clickable links to library spectra. You can launch this tool from
SpectraST Tools -> Convert Libraries to HTML.
Hope this helps,
--Luis
On Thu, Jan 21, 2021 at 12:09 AM giangiacomo beretta <
Hello James,
Yes, these values are still hard-coded. If you wish to test alternative
values, you can edit lines 958-959 and recompile:
https://sourceforge.net/p/sashimi/code/HEAD/tree/trunk/trans_proteomic_pipeline/src/Validation/ProteinProphet/ProteinProphet.cpp
MIN_WT = 0.5;
MIN_PROB =
Hello Mehar,
It seems that there was an issue with reading your user session cookie --
perhaps you followed an old link, reinstalled TPP while logged in, or your
browser does not support cookies.
I suggest starting a new browser session and try to run TPP again; let us
know if the issue persists.
Hello,
This is likely an issue with the webserver not realizing that X!Tandem has
finished running.
Can you see if there are any "tandem.exe" processes running by opening the
Task Manager?
- If you do not see any and if you can see .tandem output files, it means
that the job is done, but the
Hello Soroush,
Great! Good to verify that it is working as designed. And you will not
miss those zero probability proteins; they would just add even more time to
the processing and make a larger output file, but with no gain in high
quality results.
Cheers,
--Luis
On Tue, Nov 17, 2020 at
Hello Soroush,
ProteinProphet has baked-in defaults in the code that will skip over any
peptide with (initial) probability < 0.05 (and won't use those below 0.20
post-NSP adjustment). Do any of those peptides that point to the missing
proteins violate that rule?
This is certainly something that
Hi Miguel,
Glad that you were able to solve this, and sorry we could not help, as we
do not have access to a WS2019 machine.
Thanks for the update, and hope TPP keeps being useful to your research!
--Luis
On Mon, Nov 9, 2020 at 4:17 PM Miguel Cosenza wrote:
> Hello,
>
> I managed to solve
Hi Nathan,
In case you want to build something that closely resembles 5.2.0, you can
follow the steps on this page:
http://tools.proteomecenter.org/wiki/index.php?title=TPP_5.2.0:_Installing_on_Ubuntu_18.04_LTS
making sure to use revision 7909. Alternatively, you can use an older
compiler to
Hello Emily,
This is not a problem that we have seen much of. Do you know which version
of ProteinProphet / TPP you are using?
One potential issue is the large number of proteins (and peptides) that it
is trying to process -- can you either monitor the memory usage of the
machine when you run
The other alternative is to run XPRESS in Label-free mode. For peaks where
it can extract intensities, it will report two results: one for the
integrated area with corresponding scan range, and one for the maximum peak
intensity along with the scan number of that peak. You can view and export
This looks great! Thank you. Robert!
--Luis
On Fri, Sep 25, 2020 at 1:34 PM Robert
wrote:
> Hi, I just published a software for post-processing TPP .pepXML files
> (validated by PeptideProphet). The GUI software has the following functions:
>
> - Calculation of protein inference/
Hello Mehar,
Unfortunately PTMProphet does not calculate the protein position of the
modified amino acids; we may add this to a future version of TPP.
In the meantime, you would need to determine it from mapping the peptide
sequence onto its corresponding protein, with the caveat that the
Hi Gabby,
So since Percolator is not actually running, it just means that the
interface is confused. On that page where you see the command list, click
on "View" (instead of "Kill Job"), and at the bottom of the page that comes
up you will find a small link (at the end of "If your commands have
Hello,
Is this running on your local machine? If so, you can see if Percolator is
still running by either opening the Task Manager (if on Windows) or
executing the "ps" command (in Linux).
Most likely, the command might have timed out due a very long running time,
and the interface (Petunia) is
Hi Lindsey,
It seems that Kojak did not finish successfully, and it may be the reason
why there is no output file. If you scroll down in the command-line output
sub-window (the one in your screenshot, just scroll down more), you should
be able to see diagnostic messages that may be helpful in
Hello Alejandro,
Can you share the html source? The most likely culprit is that it has the
wrong location of the javascript files.
It may also be the case that if you re-installed TPP after you generated
the models files, they may need to be updated. The simplest way to do this
is to delete
Hello,
It seems that Lorikeet is unable to find the mzML file to extract and
display the spectrum. Did you move the files after you conducted the
analysis?
If you look at the bottom of your screenshot, you can see that the file
must be located under "/proteomics/jpanga/." Can you confirm
Hello Cindy,
Please note that raw to mzML conversion via the msconvert program only
works on Windows systems. Once the file is in the mzML format, you can
carry on with analysis on Linux.
Cheers,
--Luis
On Thu, Feb 20, 2020 at 4:48 AM Cindy Dieryckx
wrote:
> Hello,
>
> Thanks a lot but now,
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